AtlasCreator for 3D Slicer Version v0.21 3D Slicer manually specified: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --tmp_dir /var/tmp/haehn --config_dir /var/tmp/haehn Created output directory: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/ Debug Mode is enabled! Adding module path: /var/tmp/haehn/Slicer3haehn/16139/CMTK4Slicer Starting Slicer: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build [AtlasCreator 15:32:31] -------------------------------------------------------------------------------- [AtlasCreator 15:32:31] Starting Atlas Creator Normal Mode [AtlasCreator 15:32:31] Configuration for Atlas Creator: Original Images: ['/projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd'] Segmentations: ['/projects/na-mic/haehn/DATASETS/Study/segmentations/case10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case19.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case20.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case23.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case26.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case29.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case32.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case36.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case40.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case41.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case42.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case46.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case47.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case48.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case51.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case53.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case54.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case57.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case59.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case60.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case61.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case62.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/case8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG1.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG10.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG11.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG12.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG13.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG14.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG15.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG16.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG17.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG2.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG27.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG3.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG33.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG4.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG5.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG6.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG7.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG8.nrrd', '/projects/na-mic/haehn/DATASETS/Study/segmentations/caseG9.nrrd'] Output Directory: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/ Template Type: fixed Dynamic Template Iterations: 5 Fixed Template Default Case: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Labels: [32, 3, 4, 5, 6, 7, 8, 9, 10, 31] Toolkit: BRAINSFit Registration Type: Affine Save Transforms: 1 Delete Aligned Images: 0 Delete Aligned Segmentations: 0 Normalize Atlases: 0 Output Cast: Short [AtlasCreator 15:32:31] Entering Registration Stage.. [AtlasCreator 15:32:31] Found 3D Slicer launcher at /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 [AtlasCreator 15:32:31] DEBUG: The launchCommandPrefix is /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/ [AtlasCreator 15:32:31] Fixed registration against /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Background level guess : first place: 0 (99.6492%) second place: 68 (0.00519283%) Guessed background level: 0 [AtlasCreator 15:32:32] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:32:33] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:32:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 218 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 127 LowHigh Thresholds: [0,44.0234,127] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xbc16c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 0.99863 0.0511923 -0.0108813 -0.052336 0.976807 -0.207627 8.67362e-19 0.207912 0.978148 Offset: [-3.22794, -6.0867, 14.5257] Center: [0.185029, 12.049, -0.973908] Translation: [-2.60078, -6.17362, 17.0521] Inverse: 0.99863 -0.052336 8.67362e-19 0.0511923 0.976807 0.207912 -0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998862 -0.00040146 -0.0476957 -0.00969655 0.977374 -0.211296 0.0467013 0.211518 0.976258 Offset = [-2.45681, -6.6346, 14.8775] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00197 0.000614355 -0.0581304 -0.0126846 0.963764 -0.207503 0.0567329 0.207889 0.942529 Offset = [-2.78897, -6.3651, 15.141] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00473 0.00138589 -0.0425354 0.0143124 0.956497 -0.21797 0.0620471 0.1903 0.927835 Offset = [-2.89354, -6.37905, 15.3206] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 47 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00725 0.0104188 -0.0553451 0.0128908 0.958204 -0.221353 0.0570611 0.19013 0.92344 Offset = [-2.64056, -6.15732, 14.7373] Background level guess : first place: 0 (99.8355%) second place: 156 (0.00356523%) Guessed background level: 0 [AtlasCreator 15:36:59] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:36:59] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:36:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 269 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 173 LowHigh Thresholds: [0,64.1875,173] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xe396c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4066 Debug: Off Observers: none Matrix: 1 -1.38018e-17 1.45062e-18 1.38778e-17 0.994522 -0.104528 0 0.104528 0.994522 Offset: [-2.43191, -3.70288, 15.8093] Center: [0.185029, 12.049, -0.973908] Translation: [-2.43191, -3.66708, 17.0741] Inverse: 1 1.38778e-17 0 -1.38018e-17 0.994522 0.104528 1.45062e-18 -0.104528 0.994522 Singular: 0 Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999782 -0.0206685 -0.00282895 0.0201911 0.992824 -0.117868 0.00524481 0.117785 0.993025 Offset = [-2.07109, -3.50224, 15.7477] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.946071 -0.0188847 -0.0108666 0.0176284 0.977511 -0.105948 0.0128046 0.105731 0.943364 Offset = [-2.19737, -2.95061, 16.0954] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.953077 -0.0220135 -0.00308672 0.0204257 0.969777 -0.147237 0.028056 0.106638 0.943333 Offset = [-2.069, -3.27683, 16.3955] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.952722 -0.0241187 -0.00400934 0.0158813 0.972945 -0.145147 0.0242135 0.106952 0.942499 Offset = [-2.09822, -3.59556, 16.2969] Background level guess : first place: 0 (99.1645%) second place: 142 (0.0144934%) Guessed background level: 0 [AtlasCreator 15:41:14] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:41:14] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:41:14] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 261 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 167 LowHigh Thresholds: [0,59.6953,167] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1e4f6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4093 Debug: Off Observers: none Matrix: 0.994522 -0.102244 0.0217327 0.104528 0.972789 -0.206773 1.73472e-18 0.207912 0.978148 Offset: [-3.01296, -5.52692, 17.9475] Center: [0.185029, 12.049, -0.973908] Translation: [-4.26707, -5.63407, 20.4739] Inverse: 0.994522 0.104528 1.73472e-18 -0.102244 0.972789 0.207912 0.0217327 -0.206773 0.978148 Singular: 0 Versor: [ 0.104385, 0.0054706, 0.0520493, 0.993159 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.989161 -0.104755 0.102889 0.122321 0.975516 -0.182774 -0.0812238 0.193378 0.977756 Offset = [-3.06933, -5.01073, 17.9322] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.957434 -0.105572 0.102466 0.121964 0.974853 -0.169794 -0.0822764 0.180444 0.926982 Offset = [-3.23634, -5.01123, 18.4485] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.952405 -0.0980888 0.0938338 0.164585 0.972091 -0.165665 -0.0659816 0.172459 0.920972 Offset = [-2.85816, -4.92006, 18.5268] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.947994 -0.102495 0.0985647 0.172445 0.968747 -0.167777 -0.0656409 0.180539 0.929971 Offset = [-2.87401, -4.99005, 18.7135] Background level guess : first place: 0 (99.9963%) second place: 141 (0.00031002%) Guessed background level: 0 [AtlasCreator 15:45:30] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:45:30] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:45:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 377 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 226 LowHigh Thresholds: [0,85.8906,226] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x11646c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4075 Debug: Off Observers: none Matrix: 0.99863 0.0511923 -0.0108813 -0.052336 0.976807 -0.207627 8.67362e-19 0.207912 0.978148 Offset: [-3.61887, -4.21679, 21.3149] Center: [0.185029, 12.049, -0.973908] Translation: [-2.99171, -4.30372, 23.8413] Inverse: 0.99863 -0.052336 8.67362e-19 0.0511923 0.976807 0.207912 -0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.99636 0.00623909 -0.085017 -0.0260752 0.971822 -0.234271 0.0811597 0.235635 0.968447 Offset = [-3.38266, -4.2803, 20.0045] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.94771 0.0060228 -0.0874682 -0.0233371 0.909812 -0.198309 0.0845124 0.199587 0.885425 Offset = [-3.28034, -3.41814, 21.0088] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.948187 0.011867 -0.0701474 -0.0108948 0.91029 -0.191784 0.0836541 0.197345 0.878668 Offset = [-3.37337, -3.1605, 21.2932] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.949743 0.00928209 -0.0755106 -0.00306399 0.906352 -0.200638 0.0817889 0.197337 0.873871 Offset = [-3.27132, -3.12552, 21.5576] Guessed background level: 0 [AtlasCreator 15:49:43] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:49:44] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:49:44] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case19.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case19.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 331 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 220 LowHigh Thresholds: [0,81.1562,220] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x21736c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4081 Debug: Off Observers: none Matrix: 1 -1.37069e-17 2.17096e-18 1.38778e-17 0.987688 -0.156434 1.92593e-34 0.156434 0.987688 Offset: [3.99962, -1.29149, 17.6962] Center: [0.185029, 12.049, -0.973908] Translation: [3.99962, -1.28748, 19.593] Inverse: 1 1.38778e-17 1.92593e-34 -1.37069e-17 0.987688 0.156434 2.17096e-18 -0.156434 0.987688 Singular: 0 Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999431 0.00660602 -0.0330664 -0.0110455 0.990656 -0.135937 0.0318594 0.136225 0.990166 Offset = [4.46908, -0.93159, 16.4881] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.935235 0.0108025 -0.0256938 -0.0140381 0.89381 -0.129288 0.024079 0.129599 0.900974 Offset = [3.78065, -0.358398, 18.3953] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.92982 0.00604249 -0.0262509 0.000946857 0.892265 -0.127032 0.0324053 0.122325 0.904247 Offset = [3.80859, -0.118127, 18.7306] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 11 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.934928 0.0109884 -0.0377725 -0.00507334 0.895545 -0.137636 0.0431524 0.133733 0.906006 Offset = [4.00998, -0.0665706, 18.6036] Background level guess : first place: 0 (99.9893%) second place: 41 (0.00031002%) Guessed background level: 0 [AtlasCreator 15:54:02] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:54:02] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:54:02] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 245 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 157 LowHigh Thresholds: [0,57.2812,157] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xd456c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4075 Debug: Off Observers: none Matrix: 0.99863 0.0516916 -0.00818715 -0.052336 0.986335 -0.15622 8.67362e-19 0.156434 0.987688 Offset: [-2.29568, -10.3158, 8.36138] Center: [0.185029, 12.049, -0.973908] Translation: [-1.66513, -10.338, 10.2582] Inverse: 0.99863 -0.052336 8.67362e-19 0.0516916 0.986335 0.156434 -0.00818715 -0.15622 0.987688 Singular: 0 Versor: [ 0.0784322, -0.00205382, -0.0260963, 0.996576 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 45 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.996568 -0.00160426 -0.0827682 -0.00941143 0.991135 -0.132529 0.0822471 0.132853 0.987717 Offset = [-1.77184, -10.7555, 8.65445] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.951209 -0.0027061 -0.101047 -0.00703231 0.893547 -0.0958946 0.100838 0.096114 0.909322 Offset = [-1.9157, -8.53925, 9.68314] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.959225 -0.00250298 -0.105491 -0.0232207 0.890684 -0.150079 0.0907875 0.095163 0.898283 Offset = [-1.91043, -9.15466, 9.44837] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.956652 0.00334561 -0.113873 -0.0308249 0.887162 -0.146048 0.0967038 0.0938861 0.905826 Offset = [-1.80578, -8.89658, 9.39615] Background level guess : first place: 0 (99.9754%) second place: 87 (0.000697545%) Guessed background level: 0 [AtlasCreator 15:58:18] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 15:58:19] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 15:58:19] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case20.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case20.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 274 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,64.5469,176] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x22ff6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4054 Debug: Off Observers: none Matrix: 0.99863 -0.0522642 0.00273905 0.052336 0.997261 -0.0522642 4.33681e-19 0.052336 0.99863 Offset: [-2.34522, -4.00807, 25.9646] Center: [0.185029, 12.049, -0.973908] Translation: [-2.97787, -3.98049, 26.5965] Inverse: 0.99863 0.052336 4.33681e-19 -0.0522642 0.997261 0.052336 0.00273905 -0.0522642 0.99863 Singular: 0 Versor: [ 0.026168, 0.000685233, 0.026168, 0.999315 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997988 -0.0230222 -0.0590837 0.0198562 0.998364 -0.0536244 0.0602216 0.0523433 0.996812 Offset = [-2.67832, -5.05628, 25.9296] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.02002 -0.0254217 -0.0526615 0.0229304 0.936141 -0.0473835 0.0537931 0.0460949 0.913814 Offset = [-2.59402, -3.4063, 25.9092] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.01472 -0.0353928 -0.0599909 0.0855723 0.941141 -0.0191842 0.073866 0.044928 0.915262 Offset = [-2.62454, -3.58666, 26.3201] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 10 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.0213 -0.0359278 -0.0627176 0.0893198 0.953205 -0.0235216 0.0678805 0.0437538 0.9214 Offset = [-2.52856, -3.28563, 26.2182] Guessed background level: 0 [AtlasCreator 16:02:58] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:02:58] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:02:58] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case23.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case23.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 277 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 181 LowHigh Thresholds: [0,64.5703,181] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x221f6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4063 Debug: Off Observers: none Matrix: 0.99863 -0.0522642 -0.00273905 0.052336 0.997261 0.0522642 -6.50521e-19 -0.052336 0.99863 Offset: [0.103121, -1.76217, 12.9358] Center: [0.185029, 12.049, -0.973908] Translation: [-0.524195, -1.83639, 12.3065] Inverse: 0.99863 0.052336 -6.50521e-19 -0.0522642 0.997261 -0.052336 -0.00273905 0.0522642 0.99863 Singular: 0 Versor: [ -0.026168, -0.000685233, 0.026168, 0.999315 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 107 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997251 -0.0486041 -0.055937 0.0498416 0.998538 0.0209432 0.0548373 -0.0236736 0.998215 Offset = [0.44188, -3.06159, 11.6131] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 101 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.985974 -0.0343517 -0.072996 0.0372082 0.929327 0.0381388 0.0715822 -0.0407306 0.886618 Offset = [0.208064, -1.27553, 13.0765] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.989204 -0.0405078 -0.0619381 0.0602313 0.924797 0.010541 0.0741978 -0.0443477 0.884155 Offset = [-0.154062, -1.37517, 13.3101] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.983394 -0.0346862 -0.069375 0.0502573 0.915911 0.0156159 0.0732354 -0.0419583 0.887063 Offset = [-0.181601, -0.815291, 13.3549] Background level guess : first place: 0 (99.606%) second place: 143 (0.00759549%) Guessed background level: 0 [AtlasCreator 16:08:04] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:08:05] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:08:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case26.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case26.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 259 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 171 LowHigh Thresholds: [0,61.1719,171] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x23746c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4078 Debug: Off Observers: none Matrix: 0.994522 -0.103242 0.0163519 0.104528 0.982278 -0.155578 1.73472e-18 0.156434 0.987688 Offset: [-6.71474, -7.03755, 9.66159] Center: [0.185029, 12.049, -0.973908] Translation: [-7.97563, -7.08023, 11.5585] Inverse: 0.994522 0.104528 1.73472e-18 -0.103242 0.982278 0.156434 0.0163519 -0.155578 0.987688 Singular: 0 Versor: [ 0.0783516, 0.00410623, 0.0521746, 0.995551 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.994756 -0.102202 0.00385475 0.102006 0.988712 -0.109738 0.00740421 0.109556 0.993953 Offset = [-6.51107, -6.5359, 10.8126] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 64 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00488 -0.109588 0.00283061 0.109137 0.975006 -0.119732 0.010328 0.119319 0.967359 Offset = [-6.92097, -6.41139, 10.3852] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00634 -0.115463 -0.00400046 0.147541 0.972127 -0.147568 0.00475352 0.109694 0.95257 Offset = [-6.8422, -6.05129, 10.3357] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 1.00533 -0.12134 -0.00636677 0.136727 0.965459 -0.156417 -0.00229715 0.114864 0.953837 Offset = [-6.57662, -6.02798, 10.3615] Background level guess : first place: 0 (99.9778%) second place: 228 (0.00093006%) Guessed background level: 0 [AtlasCreator 16:13:02] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:13:03] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:13:03] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 340 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 240 LowHigh Thresholds: [0,89.9062,240] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1ff96c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4093 Debug: Off Observers: none Matrix: 0.987688 -0.154508 0.0244717 0.156434 0.975528 -0.154508 5.20417e-18 0.156434 0.987688 Offset: [-1.68572, -1.70193, 5.28925] Center: [0.185029, 12.049, -0.973908] Translation: [-3.5735, -1.81737, 7.18612] Inverse: 0.987688 0.156434 5.20417e-18 -0.154508 0.975528 0.156434 0.0244717 -0.154508 0.987688 Singular: 0 Versor: [ 0.0782172, 0.00615583, 0.0782172, 0.993844 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991883 -0.125655 0.0194492 0.127151 0.980436 -0.150258 -0.000188022 0.151512 0.988455 Offset = [-2.22083, -2.00083, 5.11404] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.913402 -0.114911 -0.0182944 0.11287 0.909262 -0.0885127 0.0282763 0.0858465 0.863447 Offset = [-2.40853, -0.565494, 5.91967] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.910218 -0.112938 -0.0294848 0.111042 0.916909 -0.0595416 0.0430323 0.0806562 0.857599 Offset = [-2.50256, -0.437865, 5.9797] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.911811 -0.107258 -0.0203356 0.116913 0.914272 -0.0687432 0.034421 0.0862791 0.86096 Offset = [-2.55915, -0.217752, 6.00047] Guessed background level: 0 [AtlasCreator 16:17:16] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:17:17] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:17:17] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case29.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case29.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 228 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 172 LowHigh Thresholds: [0,62.9062,172] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x203e6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4057 Debug: Off Observers: none Matrix: 1 -1.38588e-17 -7.26307e-19 1.38778e-17 0.99863 0.052336 0 -0.052336 0.99863 Offset: [-8.20385, -0.345786, 10.7269] Center: [0.185029, 12.049, -0.973908] Translation: [-8.20385, -0.413269, 10.0976] Inverse: 1 1.38778e-17 0 -1.38588e-17 0.99863 -0.052336 -7.26307e-19 0.052336 0.99863 Singular: 0 Versor: [ -0.0261769, -1.81639e-19, 6.93652e-18, 0.999657 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999161 -0.0269265 -0.0308583 0.0283123 0.998568 0.045386 0.029592 -0.0462216 0.998493 Offset = [-7.85767, -0.538338, 9.82362] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.913032 -0.0417314 -0.0761154 0.0442571 0.913454 0.0318016 0.0746752 -0.0350503 0.941043 Offset = [-8.2634, 1.05791, 10.1793] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.926897 -0.0125223 -0.0575088 -0.0211948 0.91144 -0.00916893 0.0939382 -0.0337134 0.935664 Offset = [-8.43036, 1.19684, 10.5169] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 54 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.945594 -0.0198425 -0.0382085 -0.00694715 0.929768 -0.0240131 0.0979486 -0.0342084 0.955984 Offset = [-7.87836, 0.975047, 10.8118] Background level guess : first place: 0 (99.6932%) second place: 135 (0.00364273%) Guessed background level: 0 [AtlasCreator 16:21:57] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:21:58] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:21:58] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 324 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 190 LowHigh Thresholds: [0,69.3359,190] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x22ea6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-7.00678, -3.63078, 14.7091] Center: [0.185029, 12.049, -0.973908] Translation: [-7.63445, -3.69834, 17.2355] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.99441 -0.0804923 -0.0683384 0.0670367 0.981312 -0.180369 0.0815796 0.17478 0.981222 Offset = [-6.89673, -3.64436, 15.1793] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.931877 -0.0714223 -0.0691642 0.0586753 0.955183 -0.171415 0.0802623 0.166507 0.895626 Offset = [-6.76943, -3.36233, 15.4062] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.938839 -0.0716936 -0.0671431 0.0753793 0.956871 -0.170563 0.0876168 0.16124 0.889638 Offset = [-6.91742, -3.24199, 15.6206] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.934915 -0.0666156 -0.0800842 0.0776455 0.959679 -0.171966 0.0882615 0.153434 0.893057 Offset = [-6.71696, -3.08929, 15.5676] Background level guess : first place: 0 (99.9661%) second place: 125 (0.00100756%) Guessed background level: 0 [AtlasCreator 16:26:14] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:26:14] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:26:14] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case32.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case32.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 253 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 162 LowHigh Thresholds: [0,58.4531,162] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x14816c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4060 Debug: Off Observers: none Matrix: 0.994522 -0.104385 -0.0054706 0.104528 0.993159 0.0520493 4.33681e-19 -0.052336 0.99863 Offset: [-2.70027, -3.70912, 7.69963] Center: [0.185029, 12.049, -0.973908] Translation: [-3.95369, -3.8229, 7.07037] Inverse: 0.994522 0.104528 4.33681e-19 -0.104385 0.993159 -0.052336 -0.0054706 0.0520493 0.99863 Singular: 0 Versor: [ -0.0261411, -0.00137, 0.052318, 0.998287 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 128 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.993912 -0.0738351 -0.0817743 0.0775011 0.996082 0.0425978 0.0783087 -0.0486761 0.99574 Offset = [-2.75662, -3.76338, 7.43922] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.919416 -0.081069 -0.0955917 0.086076 0.963644 0.0494675 0.0911092 -0.0573055 0.924557 Offset = [-2.95455, -3.15571, 8.26542] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.924923 -0.0929517 -0.0865357 0.116173 0.957263 0.0236759 0.0804517 -0.0839376 0.897706 Offset = [-3.18045, -3.07008, 8.46642] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.913172 -0.0905579 -0.0960813 0.109078 0.951499 0.0227379 0.0857513 -0.081026 0.906388 Offset = [-2.95092, -2.93192, 9.01929] Guessed background level: 0 [AtlasCreator 16:31:04] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:31:05] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:31:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 224 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 144 LowHigh Thresholds: [0,52.8125,144] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1a856c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4054 Debug: Off Observers: none Matrix: 1 -1.38588e-17 -7.26307e-19 1.38778e-17 0.99863 0.052336 0 -0.052336 0.99863 Offset: [3.4991, -6.29764, 4.43158] Center: [0.185029, 12.049, -0.973908] Translation: [3.4991, -6.36512, 3.80232] Inverse: 1 1.38778e-17 0 -1.38588e-17 0.99863 -0.052336 -7.26307e-19 0.052336 0.99863 Singular: 0 Versor: [ -0.0261769, -1.81639e-19, 6.93652e-18, 0.999657 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.996943 0.00230194 -0.0781003 0.00092594 0.999148 0.0412686 0.0781287 -0.0412147 0.996091 Offset = [3.1678, -6.1179, 4.01789] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.962301 0.00476171 -0.0741568 -0.00335979 0.918758 0.0190182 0.0742335 -0.0187165 0.953465 Offset = [3.39048, -5.16483, 4.06091] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.961352 3.97008e-05 -0.0939474 -0.00788974 0.912876 -0.050564 0.091977 -0.010824 0.945437 Offset = [3.42437, -5.14469, 4.64015] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.953677 0.00474975 -0.0864185 -0.0154164 0.91364 -0.0440449 0.0788442 -0.011178 0.962861 Offset = [3.32455, -5.06541, 4.37547] Background level guess : first place: 0 (99.8568%) second place: 144 (0.00224764%) Guessed background level: 0 [AtlasCreator 16:35:29] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:35:30] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:35:30] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case36.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case36.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 273 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 170 LowHigh Thresholds: [0,63,170] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xbfa6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4087 Debug: Off Observers: none Matrix: 0.978148 -0.207627 0.0108813 0.207912 0.976807 -0.0511923 -8.67362e-19 0.052336 0.99863 Offset: [-5.18117, -4.25909, 6.64037] Center: [0.185029, 12.049, -0.973908] Translation: [-7.69749, -4.45021, 7.2723] Inverse: 0.978148 0.207912 -8.67362e-19 -0.207627 0.976807 0.052336 0.0108813 -0.0511923 0.99863 Singular: 0 Versor: [ 0.0260335, 0.00273624, 0.104493, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 67 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.981566 -0.172819 0.0816185 0.175895 0.983886 -0.0320786 -0.0747595 0.0458435 0.996147 Offset = [-5.68412, -4.41573, 6.63142] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.917907 -0.173566 0.0496117 0.175347 0.972094 -0.0340987 -0.0428954 0.0422377 0.912992 Offset = [-5.76792, -3.91042, 7.39642] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.920383 -0.189394 0.0485101 0.189735 0.971308 -0.0365164 -0.0399777 0.0398139 0.90655 Offset = [-5.54278, -3.82589, 7.47191] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.917186 -0.179625 0.0433992 0.179257 0.973891 -0.0297452 -0.0389458 0.0291908 0.909322 Offset = [-5.47537, -3.94409, 7.47023] Background level guess : first place: 0 (99.9645%) second place: 127 (0.000697545%) Guessed background level: 0 [AtlasCreator 16:39:58] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:39:59] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:39:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case40.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case40.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 309 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 204 LowHigh Thresholds: [0,73.7344,204] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xe2d6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4060 Debug: Off Observers: none Matrix: 1 -1.38018e-17 1.45062e-18 1.38778e-17 0.994522 -0.104528 0 0.104528 0.994522 Offset: [1.10861, -5.56653, 2.70207] Center: [0.185029, 12.049, -0.973908] Translation: [1.10861, -5.53074, 3.96687] Inverse: 1 1.38778e-17 0 -1.38018e-17 0.994522 0.104528 1.45062e-18 -0.104528 0.994522 Singular: 0 Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.995083 -0.0157118 -0.0977868 0.00923571 0.997755 -0.0663307 0.0986095 0.0651014 0.992994 Offset = [0.715028, -6.04874, 2.74633] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 75 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.928395 -0.0348485 -0.0897678 0.0317014 0.935073 -0.0362484 0.0909268 0.0332342 0.92685 Offset = [1.3256, -4.29516, 4.2004] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.933305 -0.0394959 -0.0742792 0.0569936 0.925691 -0.0840092 0.0668033 0.0286049 0.919343 Offset = [1.43696, -4.34336, 4.48507] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.927491 -0.0229984 -0.0705947 0.0554456 0.920096 -0.0898005 0.0785091 0.0347442 0.918927 Offset = [1.0091, -4.43246, 4.17616] Background level guess : first place: 0 (99.8872%) second place: 69 (0.00271267%) Guessed background level: 0 [AtlasCreator 16:44:36] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:44:37] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:44:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case41.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case41.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 237 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 139 LowHigh Thresholds: [0,50.0625,139] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x15076c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4057 Debug: Off Observers: none Matrix: 1 -1.38018e-17 1.45062e-18 1.38778e-17 0.994522 -0.104528 0 0.104528 0.994522 Offset: [-4.96739, -3.76571, 5.58953] Center: [0.185029, 12.049, -0.973908] Translation: [-4.96739, -3.72991, 6.85433] Inverse: 1 1.38778e-17 0 -1.38018e-17 0.994522 0.104528 1.45062e-18 -0.104528 0.994522 Singular: 0 Versor: [ 0.052336, 3.63154e-19, 6.92938e-18, 0.99863 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999828 -0.0160539 0.00929262 0.0166257 0.997738 -0.0651346 -0.00822593 0.0652779 0.997833 Offset = [-4.74764, -4.00902, 5.68695] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.942833 -0.0419963 0.000199296 0.0419279 0.953293 -0.0619995 0.00240501 0.0619532 0.913332 Offset = [-4.55924, -3.33529, 6.48919] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.946584 -0.0375425 -0.00554542 0.0421602 0.953352 -0.0699513 -0.00865417 0.0403048 0.912532 Offset = [-4.54361, -3.49368, 6.67428] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.944368 -0.0442847 -0.0136045 0.0536287 0.952675 -0.0783579 -0.0051896 0.043632 0.910039 Offset = [-4.34984, -3.42538, 6.60414] Guessed background level: 0 [AtlasCreator 16:49:13] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:49:14] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:49:14] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case42.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case42.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 299 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 190 LowHigh Thresholds: [0,70.1172,190] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1ea66c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4054 Debug: Off Observers: none Matrix: 0.99863 -0.052336 7.26307e-19 0.052336 0.99863 -1.38588e-17 0 1.38778e-17 1 Offset: [-1.09545, -3.8282, -1.38892] Center: [0.185029, 12.049, -0.973908] Translation: [-1.7263, -3.83502, -1.38892] Inverse: 0.99863 0.052336 0 -0.052336 0.99863 1.38778e-17 7.26307e-19 -1.38588e-17 1 Singular: 0 Versor: [ 6.93652e-18, 1.81639e-19, 0.0261769, 0.999657 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998833 -0.0441462 -0.0196008 0.0441462 0.999025 -0.000432291 0.0196008 -0.000433515 0.999808 Offset = [-1.20906, -4.09278, -1.60161] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.928468 -0.0394046 -0.0569071 0.0401064 0.948014 0.0112439 0.0564146 -0.0134993 0.922111 Offset = [-1.58949, -2.86891, -1.0077] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.930443 -0.0539233 -0.0578264 0.0515396 0.943486 0.00568239 0.058792 -0.0302121 0.909004 Offset = [-1.38678, -2.69508, -1.2242] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.929087 -0.0405786 -0.0612786 0.0412474 0.944981 -9.16792e-06 0.04895 -0.0346861 0.913611 Offset = [-1.4602, -2.51369, -1.04251] Background level guess : first place: 0 (99.7911%) second place: 120 (0.00356523%) Guessed background level: 0 [AtlasCreator 16:53:43] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:53:44] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:53:44] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case46.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case46.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 226 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 150 LowHigh Thresholds: [0,54.4219,150] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x22366c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4078 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [3.4984, -5.14359, 15.2604] Center: [0.185029, 12.049, -0.973908] Translation: [2.87073, -5.21115, 17.7868] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999468 -0.0304783 0.0115893 0.0326019 0.940516 -0.338181 -0.000592723 0.338379 0.94101 Offset = [3.7569, -4.22284, 12.5971] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.950268 -0.0442874 -0.000261723 0.0421504 0.915129 -0.301312 0.0135936 0.301005 0.916832 Offset = [3.35151, -4.17527, 13.9516] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 17 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.952354 -0.038083 0.00298003 0.0191242 0.917254 -0.301369 -0.00617756 0.311642 0.914737 Offset = [3.69554, -4.03852, 13.9741] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.951017 -0.0442006 -0.00717048 0.0195871 0.923083 -0.289306 0.00546643 0.298643 0.920672 Offset = [3.60635, -3.53884, 13.9756] Guessed background level: 0 [AtlasCreator 16:57:56] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 16:57:56] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 16:57:56] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case47.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case47.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 287 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 173 LowHigh Thresholds: [0,63.25,173] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x21646c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-7.12609, -8.47309, 16.8928] Center: [0.185029, 12.049, -0.973908] Translation: [-7.75376, -8.54065, 19.4192] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998618 -0.0521309 0.00672302 0.0523656 0.975639 -0.213041 0.00454674 0.213098 0.97702 Offset = [-7.0014, -8.65867, 16.1916] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.96271 -0.0345329 -0.0247959 0.0289586 0.856045 -0.197761 0.0311249 0.196865 0.916946 Offset = [-7.58353, -6.98422, 16.8431] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.964903 -0.0414963 -0.0208898 0.0813545 0.86411 -0.183436 0.034056 0.214801 0.914624 Offset = [-7.4293, -6.86102, 17.0113] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.962937 -0.0476607 -0.0257971 0.0867791 0.866627 -0.179767 0.0298011 0.207926 0.910757 Offset = [-7.14386, -6.76893, 17.2155] Guessed background level: 0 [AtlasCreator 17:02:17] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:02:18] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:02:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case48.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case48.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 205 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 133 LowHigh Thresholds: [0,47.8047,133] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x24f06c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4081 Debug: Off Observers: none Matrix: 0.99863 0.0511923 -0.0108813 -0.052336 0.976807 -0.207627 8.67362e-19 0.207912 0.978148 Offset: [-1.29775, -5.32743, 5.13828] Center: [0.185029, 12.049, -0.973908] Translation: [-0.670596, -5.41436, 7.66468] Inverse: 0.99863 -0.052336 8.67362e-19 0.0511923 0.976807 0.207912 -0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.994986 0.0572685 -0.0819891 -0.0695763 0.985281 -0.156142 0.0718403 0.161064 0.984326 Offset = [-1.47383, -6.25428, 5.43618] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 71 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.971083 0.0345027 -0.0727377 -0.0447173 0.909125 -0.143848 0.0669446 0.146633 0.915868 Offset = [-0.791699, -4.90632, 6.38005] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.971205 0.0340933 -0.0733197 0.00281183 0.899091 -0.202862 0.0710924 0.127748 0.891221 Offset = [-0.785291, -4.33748, 7.23997] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.973469 0.0250908 -0.0905738 0.000182149 0.899339 -0.20158 0.0843249 0.13811 0.887303 Offset = [-0.498377, -4.51086, 7.22094] Background level guess : first place: 0 (99.5194%) second place: 159 (0.00658792%) Guessed background level: 0 [AtlasCreator 17:07:04] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:07:05] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:07:05] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case51.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case51.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 265 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 174 LowHigh Thresholds: [0,63.7031,174] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x28ec6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4075 Debug: Off Observers: none Matrix: 1 -1.35745e-17 2.88535e-18 1.38778e-17 0.978148 -0.207912 1.92593e-34 0.207912 0.978148 Offset: [0.194642, -7.80573, 23.9528] Center: [0.185029, 12.049, -0.973908] Translation: [0.194642, -7.86654, 26.4792] Inverse: 1 1.38778e-17 1.92593e-34 -1.35745e-17 0.978148 0.207912 2.88535e-18 -0.207912 0.978148 Singular: 0 Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 24 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999996 0.002195 0.00157156 -0.00165648 0.95858 -0.284819 -0.00213164 0.284815 0.95858 Offset = [0.692034, -7.30601, 22.5207] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 46 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.943528 0.00136691 -9.91875e-07 -0.00130634 0.931889 -0.295069 -0.000402385 0.295069 0.925743 Offset = [0.346197, -7.4296, 23.5443] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.934344 0.00352681 0.00971507 -0.0036923 0.93431 -0.295512 0.0148414 0.29179 0.913123 Offset = [0.301586, -7.27079, 23.7603] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 48 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.934932 -0.00143926 0.000254072 0.0101036 0.933819 -0.278071 0.0260277 0.286181 0.937402 Offset = [0.262148, -7.18383, 23.8645] Background level guess : first place: 0 (99.921%) second place: 111 (0.00124008%) Guessed background level: 0 [AtlasCreator 17:11:32] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:11:33] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:11:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case53.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case53.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 309 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 195 LowHigh Thresholds: [0,72.1875,195] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xc596c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 0.99863 0.0511923 -0.0108813 -0.052336 0.976807 -0.207627 8.67362e-19 0.207912 0.978148 Offset: [-0.621802, -4.28221, 9.30782] Center: [0.185029, 12.049, -0.973908] Translation: [0.00535623, -4.36914, 11.8342] Inverse: 0.99863 -0.052336 8.67362e-19 0.0511923 0.976807 0.207912 -0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999407 0.0080058 -0.0334992 -0.0145112 0.979947 -0.198731 0.0312364 0.199099 0.979481 Offset = [-0.0324082, -4.39457, 9.54256] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 41 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.97863 -0.0043324 -0.0434654 -0.00270227 0.939081 -0.160493 0.0435972 0.160458 0.942612 Offset = [-0.0468679, -3.34013, 10.3122] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.982494 -0.000988913 -0.0371715 0.0070913 0.939094 -0.171025 0.0412723 0.155429 0.937792 Offset = [-0.11787, -3.07008, 10.6498] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.980612 -0.00266723 -0.0394079 0.0162405 0.943743 -0.16847 0.0340692 0.150964 0.942993 Offset = [0.103982, -2.94995, 10.5082] Guessed background level: 0 [AtlasCreator 17:15:58] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:15:59] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:15:59] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case54.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case54.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 295 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 196 LowHigh Thresholds: [0,73.4062,196] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x194d6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4066 Debug: Off Observers: none Matrix: 0.99863 0.0520493 -0.0054706 -0.052336 0.993159 -0.104385 4.33681e-19 0.104528 0.994522 Offset: [-5.29963, 0.10532, 12.7761] Center: [0.185029, 12.049, -0.973908] Translation: [-4.66741, 0.11487, 14.0409] Inverse: 0.99863 -0.052336 4.33681e-19 0.0520493 0.993159 0.104528 -0.0054706 -0.104385 0.994522 Singular: 0 Versor: [ 0.052318, -0.00137, -0.0261411, 0.998287 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 69 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999892 0.0061953 0.0133518 -0.00491485 0.995571 -0.0938854 -0.0138744 0.0938097 0.995493 Offset = [-4.75918, 0.0649319, 11.7663] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 61 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.923657 -0.0206672 -0.0225043 0.0201168 0.871232 -0.0244172 0.0229977 0.023953 0.880175 Offset = [-4.5699, 2.17524, 13.6375] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.929184 -0.0177503 -0.0224781 0.021973 0.865939 -0.0441929 0.031509 0.0102953 0.879094 Offset = [-4.72088, 2.21153, 13.7747] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.924647 -0.0216507 -0.015157 0.0240413 0.872179 -0.0408274 0.0135198 0.00964869 0.878945 Offset = [-4.48952, 2.0393, 14.1934] Background level guess : first place: 0 (99.8487%) second place: 86 (0.00263517%) Guessed background level: 0 [AtlasCreator 17:20:42] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:20:43] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:20:43] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case57.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case57.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 264 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 169 LowHigh Thresholds: [0,60.8125,169] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xf8d6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4087 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-2.9635, -5.65829, 16.5031] Center: [0.185029, 12.049, -0.973908] Translation: [-3.59117, -5.72585, 19.0295] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998857 -0.0475272 0.00503197 0.0472042 0.964601 -0.259456 0.00747738 0.259397 0.965742 Offset = [-2.80985, -5.94463, 15.0362] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 44 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.968645 -0.0554442 -0.00217459 0.0535528 0.907712 -0.223752 0.014522 0.223291 0.888168 Offset = [-2.83574, -4.73704, 16.275] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.959126 -0.0568234 -0.00385811 0.0709434 0.918071 -0.217342 0.0321074 0.202845 0.882287 Offset = [-2.85514, -4.56395, 16.4811] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.96281 -0.0495921 -0.00546644 0.0579784 0.916241 -0.218267 0.0300367 0.204964 0.893779 Offset = [-2.47631, -4.46311, 16.5106] Guessed background level: 0 [AtlasCreator 17:25:00] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:25:01] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:25:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case59.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case59.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 277 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 193 LowHigh Thresholds: [0,70.0312,193] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x18746c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4078 Debug: Off Observers: none Matrix: 0.99863 0.0511923 -0.0108813 -0.052336 0.976807 -0.207627 8.67362e-19 0.207912 0.978148 Offset: [-0.308292, -5.58445, 12.3839] Center: [0.185029, 12.049, -0.973908] Translation: [0.318866, -5.67138, 14.9103] Inverse: 0.99863 -0.052336 8.67362e-19 0.0511923 0.976807 0.207912 -0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999633 0.0229813 -0.0143266 -0.0253166 0.98086 -0.193061 0.00961555 0.193353 0.981082 Offset = [0.133056, -5.84387, 12.315] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 81 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.955454 0.00717928 -0.0200341 -0.0109288 0.88525 -0.193853 0.0182611 0.194028 0.918615 Offset = [0.235035, -4.48193, 12.8995] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.954981 0.0170768 -0.0312101 0.0176938 0.891499 -0.176872 0.0195247 0.166912 0.905574 Offset = [0.0401444, -4.33375, 13.7828] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.949704 0.0133094 -0.0308314 0.0211807 0.890885 -0.157268 0.0145253 0.171044 0.910553 Offset = [0.195838, -4.37818, 13.711] Guessed background level: 0 [AtlasCreator 17:29:37] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:29:38] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:29:38] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case60.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case60.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 338 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 239 LowHigh Thresholds: [0,90.25,239] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x15fe6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 1 -1.37069e-17 2.17096e-18 1.38778e-17 0.987688 -0.156434 1.92593e-34 0.156434 0.987688 Offset: [-3.42715, -3.87479, 15.0139] Center: [0.185029, 12.049, -0.973908] Translation: [-3.42715, -3.87078, 16.9108] Inverse: 1 1.38778e-17 1.92593e-34 -1.37069e-17 0.987688 0.156434 2.17096e-18 -0.156434 0.987688 Singular: 0 Versor: [ 0.0784591, 5.44419e-19, 6.9175e-18, 0.996917 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 66 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998455 -0.00194936 -0.0555374 -0.00588401 0.990058 -0.140534 0.0552593 0.140644 0.988517 Offset = [-3.73328, -4.21017, 14.5932] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.913248 -0.0202889 -0.103618 0.014317 0.917951 -0.0580561 0.10461 0.0562481 0.872161 Offset = [-3.243, -2.61392, 16.1991] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.916916 -0.01438 -0.0958752 0.0205512 0.916612 -0.0984409 0.0924769 0.0542919 0.858038 Offset = [-3.28775, -2.48345, 16.3001] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.916146 -0.0132554 -0.101606 0.0232215 0.907757 -0.0960184 0.0934496 0.0524927 0.857332 Offset = [-3.16096, -2.44466, 16.2752] Background level guess : first place: 0 (99.929%) second place: 112 (0.00186012%) Guessed background level: 0 [AtlasCreator 17:34:00] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:34:00] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:34:00] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case61.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case61.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 237 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 150 LowHigh Thresholds: [0,53.9062,150] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x247d6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4081 Debug: Off Observers: none Matrix: 0.994522 -0.102244 0.0217327 0.104528 0.972789 -0.206773 1.73472e-18 0.207912 0.978148 Offset: [-1.97698, -9.23886, 21.2366] Center: [0.185029, 12.049, -0.973908] Translation: [-3.2311, -9.346, 23.763] Inverse: 0.994522 0.104528 1.73472e-18 -0.102244 0.972789 0.207912 0.0217327 -0.206773 0.978148 Singular: 0 Versor: [ 0.104385, 0.0054706, 0.0520493, 0.993159 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 80 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.996568 -0.0587119 0.0583585 0.0767804 0.919089 -0.386497 -0.0309446 0.389651 0.920442 Offset = [-2.71408, -8.67076, 17.7229] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.99005 -0.0583222 0.033134 0.0665764 0.85884 -0.383136 -0.00818061 0.384479 0.886976 Offset = [-2.57054, -7.62212, 18.9959] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.987123 -0.0539927 0.0335634 0.0759959 0.850025 -0.395691 -0.00883056 0.379662 0.88038 Offset = [-2.48301, -7.3866, 18.9747] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991931 -0.0506053 0.0285934 0.0863513 0.849994 -0.406393 -0.0100212 0.381228 0.87735 Offset = [-2.4604, -7.48815, 18.9866] Background level guess : first place: 0 (99.9685%) second place: 147 (0.000852555%) Guessed background level: 0 [AtlasCreator 17:38:25] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:38:26] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:38:26] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case62.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case62.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 252 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 170 LowHigh Thresholds: [0,62.1562,170] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x19cd6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 0.99863 -0.0516916 0.00818715 0.052336 0.986335 -0.15622 0 0.156434 0.987688 Offset: [-4.60825, -0.391146, 15.8922] Center: [0.185029, 12.049, -0.973908] Translation: [-5.2393, -0.393971, 17.7891] Inverse: 0.99863 0.052336 0 -0.0516916 0.986335 0.156434 0.00818715 -0.15622 0.987688 Singular: 0 Versor: [ 0.0784322, 0.00205382, 0.0260963, 0.996576 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 63 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997274 -0.0666912 -0.0315789 0.0606108 0.984443 -0.164922 0.0420865 0.162558 0.985801 Offset = [-3.8284, -1.56831, 15.2563] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.959571 -0.058898 -0.0254796 0.0555918 0.898136 -0.115255 0.0320584 0.113601 0.900575 Offset = [-4.49742, 0.508594, 17.0038] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.960504 -0.0642058 -0.0472595 0.0684366 0.891898 -0.154441 0.0315971 0.108592 0.894538 Offset = [-4.31621, 0.751753, 16.8098] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.958667 -0.0663702 -0.036588 0.0606151 0.887146 -0.150415 0.0254359 0.104975 0.890168 Offset = [-4.49735, 0.620619, 17.024] Background level guess : first place: 0 (99.5161%) second place: 137 (0.00713046%) Guessed background level: 0 [AtlasCreator 17:42:55] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:42:56] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:42:56] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/case8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/case8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 263 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 160 LowHigh Thresholds: [0,58.2422,160] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x237a6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4090 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-0.9092, -7.73937, 23.6615] Center: [0.185029, 12.049, -0.973908] Translation: [-1.53687, -7.80692, 26.1879] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 105 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997909 -0.0512787 -0.0393537 0.0417604 0.976156 -0.213015 0.0493385 0.210927 0.976256 Offset = [-0.388138, -7.03803, 22.9985] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.876353 -0.069748 -0.0560505 0.0588279 0.965733 -0.177163 0.067422 0.173155 0.891149 Offset = [-0.806253, -6.51146, 23.7996] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.871377 -0.0918577 -0.0556348 0.0776146 0.961408 -0.19836 0.0523042 0.172369 0.889683 Offset = [-0.572461, -6.43701, 23.707] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.88066 -0.0832487 -0.0496703 0.0749344 0.967323 -0.181822 0.0430746 0.179247 0.900013 Offset = [-0.628534, -6.4825, 23.7582] Background level guess : first place: 0 (99.7564%) second place: 38 (0.00302269%) Guessed background level: 0 [AtlasCreator 17:47:33] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:47:33] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:47:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG1.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG1.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 347 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 234 LowHigh Thresholds: [0,86.4844,234] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xc426c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4075 Debug: Off Observers: none Matrix: 0.99863 0.0516916 -0.00818715 -0.052336 0.986335 -0.15622 8.67362e-19 0.156434 0.987688 Offset: [-0.855109, -7.36495, 21.6461] Center: [0.185029, 12.049, -0.973908] Translation: [-0.224558, -7.38715, 23.543] Inverse: 0.99863 -0.052336 8.67362e-19 0.0516916 0.986335 0.156434 -0.00818715 -0.15622 0.987688 Singular: 0 Versor: [ 0.0784322, -0.00205382, -0.0260963, 0.996576 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991751 -0.00613986 -0.12803 -0.0147235 0.986783 -0.161374 0.127329 0.161928 0.978553 Offset = [-0.180788, -6.82716, 20.9608] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.931181 0.0026572 -0.138429 -0.0230886 0.960412 -0.1462 0.136515 0.147988 0.946994 Offset = [-0.344562, -6.30761, 21.6818] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.941617 0.000546111 -0.125867 0.0235318 0.969911 -0.107609 0.11971 0.148803 0.949727 Offset = [-0.151361, -6.19805, 21.7836] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.937692 -0.00400876 -0.130975 0.028002 0.969787 -0.106323 0.132071 0.150689 0.955962 Offset = [-0.0381717, -5.78898, 21.743] Background level guess : first place: 0 (99.7627%) second place: 186 (0.00410776%) Guessed background level: 0 [AtlasCreator 17:51:45] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:51:46] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:51:46] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG10.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG10.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 336 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 215 LowHigh Thresholds: [0,80.8828,215] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1ea7340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4090 Debug: Off Observers: none Matrix: 0.994522 -0.102244 0.0217327 0.104528 0.972789 -0.206773 1.73472e-18 0.207912 0.978148 Offset: [2.79727, -3.9929, 32.5321] Center: [0.185029, 12.049, -0.973908] Translation: [1.54316, -4.10004, 35.0585] Inverse: 0.994522 0.104528 1.73472e-18 -0.102244 0.972789 0.207912 0.0217327 -0.206773 0.978148 Singular: 0 Versor: [ 0.104385, 0.0054706, 0.0520493, 0.993159 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991958 -0.117391 -0.0473119 0.102995 0.965955 -0.237323 0.0735609 0.230542 0.970278 Offset = [2.82381, -3.71534, 32.1746] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.926523 -0.0970144 -0.0312271 0.0884282 0.93525 -0.208789 0.0506693 0.20494 0.91278 Offset = [2.49149, -3.23334, 33.0481] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.928858 -0.107071 -0.0395746 0.110494 0.921869 -0.257436 0.056704 0.189888 0.90111 Offset = [2.55913, -3.26971, 33.1184] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 16 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.928779 -0.105296 -0.0470152 0.116561 0.921884 -0.261012 0.0578156 0.191609 0.897759 Offset = [2.96503, -3.26338, 33.0162] Background level guess : first place: 0 (99.8225%) second place: 6 (0.00767299%) Guessed background level: 0 [AtlasCreator 17:55:50] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 17:55:51] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 17:55:51] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG11.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG11.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 332 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 229 LowHigh Thresholds: [0,85.7344,229] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x279d340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 1 -1.35745e-17 2.88535e-18 1.38778e-17 0.978148 -0.207912 1.92593e-34 0.207912 0.978148 Offset: [1.7153, -7.17869, 25.5023] Center: [0.185029, 12.049, -0.973908] Translation: [1.7153, -7.2395, 28.0287] Inverse: 1 1.38778e-17 1.92593e-34 -1.35745e-17 0.978148 0.207912 2.88535e-18 -0.207912 0.978148 Singular: 0 Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 84 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999872 -0.00652952 0.0146285 0.00951719 0.976662 -0.214569 -0.0128861 0.214681 0.976599 Offset = [1.98629, -6.94774, 24.6394] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 49 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.926816 -0.0107707 -0.00133827 0.0103542 0.918385 -0.179914 0.00325415 0.179889 0.920429 Offset = [2.1027, -6.26205, 26.0107] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.928281 -0.00845579 -0.00303192 0.0111759 0.918331 -0.192298 0.00196461 0.184115 0.911085 Offset = [1.93232, -6.10224, 25.8865] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 56 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.925446 -0.00861065 -0.000240494 0.0120971 0.917225 -0.190698 -0.00868882 0.175952 0.912749 Offset = [1.97387, -5.80734, 26.2012] Guessed background level: 0 [AtlasCreator 18:00:35] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:00:36] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:00:36] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG12.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG12.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 321 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 226 LowHigh Thresholds: [0,85.5,226] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1141340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4090 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-2.49715, -5.19953, 17.0687] Center: [0.185029, 12.049, -0.973908] Translation: [-3.12482, -5.26709, 19.5951] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 73 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997983 -0.0633872 0.00356631 0.0629043 0.979659 -0.190556 0.00858506 0.190396 0.98167 Offset = [-2.23211, -5.48139, 17.4709] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 83 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.896283 -0.0408904 0.0139054 0.0424407 0.883804 -0.140475 -0.00801079 0.140934 0.877029 Offset = [-2.48887, -3.67333, 17.9828] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.903387 -0.0377786 -0.00855951 0.0173634 0.879126 -0.174573 0.00188154 0.127358 0.863384 Offset = [-2.75293, -3.41616, 18.2282] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 52 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.903978 -0.0408853 -0.00235519 0.0265773 0.878696 -0.168673 -0.00704629 0.126569 0.872022 Offset = [-2.78256, -3.7083, 18.0845] Background level guess : first place: 0 (99.7555%) second place: 81 (0.00325521%) Guessed background level: 0 [AtlasCreator 18:05:38] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:05:39] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:05:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG13.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG13.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 336 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 229 LowHigh Thresholds: [0,85.0938,229] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1d8f340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4093 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-2.41348, -5.75356, 27.965] Center: [0.185029, 12.049, -0.973908] Translation: [-3.04115, -5.82111, 30.4914] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 40 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998179 -0.0552772 0.0241612 0.0587511 0.981677 -0.181271 -0.0136983 0.182361 0.983136 Offset = [-2.11801, -5.50582, 27.4107] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 88 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.97196 -0.0420234 0.0359643 0.0479517 0.949815 -0.184146 -0.0275688 0.185589 0.931537 Offset = [-2.32914, -5.34797, 28.1722] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.969467 -0.0527163 0.0251822 0.0930655 0.946054 -0.184147 -0.00810886 0.163769 0.922325 Offset = [-2.17579, -5.17687, 28.9476] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 37 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.97124 -0.0466449 0.029779 0.0738416 0.94424 -0.19482 -0.0254403 0.171573 0.925805 Offset = [-2.22809, -5.05454, 28.596] Background level guess : first place: 0 (98.828%) second place: 187 (0.0134859%) Guessed background level: 0 [AtlasCreator 18:10:12] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:10:13] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:10:13] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG14.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG14.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 348 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 223 LowHigh Thresholds: [0,80.2812,223] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x2673340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4075 Debug: Off Observers: none Matrix: 1 -1.35745e-17 2.88535e-18 1.38778e-17 0.978148 -0.207912 1.92593e-34 0.207912 0.978148 Offset: [1.40384, -5.29966, 29.713] Center: [0.185029, 12.049, -0.973908] Translation: [1.40384, -5.36047, 32.2394] Inverse: 1 1.38778e-17 1.92593e-34 -1.35745e-17 0.978148 0.207912 2.88535e-18 -0.207912 0.978148 Singular: 0 Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.99961 -0.0256615 -0.0110005 0.0203538 0.939472 -0.342022 0.0191115 0.341664 0.939628 Offset = [1.70568, -5.03301, 29.2788] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 39 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.977681 -0.0312647 -0.00622654 0.0270223 0.93835 -0.354842 0.0169129 0.354493 0.95979 Offset = [1.62318, -4.76308, 28.8836] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.981941 -0.0307077 -0.0185423 0.0506415 0.949355 -0.34079 0.018148 0.342198 0.955887 Offset = [1.56967, -4.74714, 29.1149] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.96961 -0.0362378 -0.017971 0.0668992 0.952475 -0.341833 0.0186858 0.351213 0.959659 Offset = [1.72168, -4.71859, 29.2145] Background level guess : first place: 0 (99.838%) second place: 81 (0.00387525%) Guessed background level: 0 [AtlasCreator 18:14:23] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:14:24] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:14:24] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG15.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG15.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 186 LowHigh Thresholds: [0,69.8438,186] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x283f340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4069 Debug: Off Observers: none Matrix: 0.994522 -0.104385 0.0054706 0.104528 0.993159 -0.0520493 -8.67362e-19 0.052336 0.99863 Offset: [-0.309016, -6.37712, 13.4963] Center: [0.185029, 12.049, -0.973908] Translation: [-1.57309, -6.38952, 14.1282] Inverse: 0.994522 0.104528 -8.67362e-19 -0.104385 0.993159 0.052336 0.0054706 -0.0520493 0.99863 Singular: 0 Versor: [ 0.0261411, 0.00137, 0.052318, 0.998287 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.993406 -0.096861 -0.0613353 0.0953274 0.995067 -0.0274615 0.0636927 0.0214335 0.997739 Offset = [-0.147841, -5.89995, 13.6267] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.958189 -0.0879948 -0.0489455 0.0869483 0.946429 -0.0231191 0.0507814 0.0187459 0.98477 Offset = [-0.249918, -4.96322, 14.1496] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.95556 -0.0686042 -0.0554197 0.132849 0.943873 -0.0751025 0.0563526 0.0138806 0.972857 Offset = [-0.41325, -4.97841, 14.4015] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.953201 -0.0854313 -0.0658858 0.153746 0.938967 -0.0683958 0.0608465 0.000901812 0.973629 Offset = [-0.315079, -4.8425, 14.2734] Guessed background level: 0 [AtlasCreator 18:19:10] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:19:10] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:19:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG16.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG16.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 337 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 225 LowHigh Thresholds: [0,84.6094,225] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x142c340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4078 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-3.06856, -5.29509, 11.781] Center: [0.185029, 12.049, -0.973908] Translation: [-3.69622, -5.36265, 14.3074] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997732 -0.0441403 -0.0508149 0.0324848 0.976983 -0.210827 0.0589513 0.208698 0.976202 Offset = [-3.21862, -5.29559, 11.5394] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 206 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.871521 -0.075562 -0.0730846 0.0635253 0.861672 -0.154917 0.0837587 0.149416 0.847717 Offset = [-2.79952, -3.13913, 12.8816] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 95 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.879505 -0.0639398 -0.0749247 0.0733802 0.847712 -0.191212 0.0803879 0.144617 0.851173 Offset = [-3.13815, -3.45888, 12.8902] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 42 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.880121 -0.0625803 -0.0786766 0.0743109 0.84983 -0.198869 0.080788 0.146722 0.844137 Offset = [-2.86112, -3.41985, 12.8412] Background level guess : first place: 0 (99.6543%) second place: 214 (0.00496032%) Guessed background level: 0 [AtlasCreator 18:24:48] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:24:48] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:24:48] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG17.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG17.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 373 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 246 LowHigh Thresholds: [0,90.8516,246] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x2825340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4075 Debug: Off Observers: none Matrix: 1 -1.35745e-17 2.88535e-18 1.38778e-17 0.978148 -0.207912 1.92593e-34 0.207912 0.978148 Offset: [3.33058, -4.81703, 30.3297] Center: [0.185029, 12.049, -0.973908] Translation: [3.33058, -4.87784, 32.8561] Inverse: 1 1.38778e-17 1.92593e-34 -1.35745e-17 0.978148 0.207912 2.88535e-18 -0.207912 0.978148 Singular: 0 Versor: [ 0.104528, 7.25312e-19, 6.90088e-18, 0.994522 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.999935 0.00701556 -0.00899954 -0.00925418 0.959994 -0.279868 0.00667607 0.279933 0.959996 Offset = [3.09059, -4.00686, 29.4945] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.953917 0.0121159 -0.0145931 -0.0156581 0.928027 -0.274543 0.0107042 0.274722 0.922413 Offset = [2.99153, -3.51897, 29.684] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.957609 0.00858806 -0.0178143 0.00418013 0.93074 -0.291948 -0.00521941 0.268697 0.916859 Offset = [3.17958, -3.74638, 29.6944] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 29 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.95173 0.00768505 -0.0254531 0.00453665 0.925228 -0.313304 0.00269409 0.262567 0.91 Offset = [3.49125, -3.4717, 29.8055] Guessed background level: 0 [AtlasCreator 18:29:02] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:29:03] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:29:03] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG2.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG2.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 280 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 201 LowHigh Thresholds: [0,73.75,201] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xc776c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4063 Debug: Off Observers: none Matrix: 0.987688 0.15622 -0.00818715 -0.156434 0.986335 -0.0516916 0 0.052336 0.99863 Offset: [1.21385, -4.85486, 14.3272] Center: [0.185029, 12.049, -0.973908] Translation: [3.10184, -4.99812, 14.9592] Inverse: 0.987688 -0.156434 0 0.15622 0.986335 0.052336 -0.00818715 -0.0516916 0.99863 Singular: 0 Versor: [ 0.0260963, -0.00205382, -0.0784322, 0.996576 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 161 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.991768 0.0555639 -0.115366 -0.0553379 0.998454 0.00516334 0.115474 0.00126327 0.99331 Offset = [1.92256, -5.20908, 14.3696] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.975621 0.0335394 -0.113135 -0.0324474 0.931325 0.0114809 0.113453 -0.00772979 0.959202 Offset = [2.49621, -3.71831, 15.0102] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.983253 0.0316108 -0.124346 0.046929 0.927003 -0.0143192 0.0918162 -0.00367101 0.945934 Offset = [2.71866, -4.00887, 15.413] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.982339 0.0345139 -0.123607 0.0491902 0.923821 -0.0223597 0.0908896 0.00741406 0.949883 Offset = [2.74352, -4.03881, 15.6964] Guessed background level: 0 [AtlasCreator 18:34:00] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:34:01] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:34:01] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG27.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG27.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 266 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 177 LowHigh Thresholds: [0,66.2812,177] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x15ee340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4063 Debug: Off Observers: none Matrix: 0.99863 -0.0522642 -0.00273905 0.052336 0.997261 0.0522642 -6.50521e-19 -0.052336 0.99863 Offset: [0.643897, -4.3604, 16.4632] Center: [0.185029, 12.049, -0.973908] Translation: [0.0165815, -4.43462, 15.8339] Inverse: 0.99863 0.052336 -6.50521e-19 -0.0522642 0.997261 -0.052336 -0.00273905 0.0522642 0.99863 Singular: 0 Versor: [ -0.026168, -0.000685233, 0.026168, 0.999315 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 68 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998124 -0.0523683 -0.0317131 0.0536876 0.997662 0.042285 0.0294246 -0.0439083 0.998602 Offset = [1.03778, -4.30519, 15.6145] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 23 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.987322 -0.0425719 -0.0313298 0.0429533 0.927043 0.0116016 0.0308048 -0.0129311 0.933186 Offset = [0.74688, -3.43059, 16.5084] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.978107 -0.0453046 -0.0346883 0.0594069 0.93657 -0.00670057 0.0230158 -0.0313122 0.919629 Offset = [0.999549, -3.63762, 17.0348] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.982548 -0.0503974 -0.045805 0.0618981 0.927571 -0.0144257 0.017961 -0.0348197 0.92761 Offset = [0.97159, -3.39216, 17.0981] Background level guess : first place: 0 (99.81%) second place: 65 (0.00279018%) Guessed background level: 0 [AtlasCreator 18:38:32] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:38:33] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:38:33] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG3.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG3.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 294 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 193 LowHigh Thresholds: [0,69.1875,193] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xd1a6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4090 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [2.68897, -3.43311, 31.3779] Center: [0.185029, 12.049, -0.973908] Translation: [2.0613, -3.50067, 33.9043] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.996841 -0.0701257 -0.0373005 0.0598383 0.971839 -0.227921 0.0522332 0.224969 0.972965 Offset = [2.84954, -3.39154, 30.1694] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 26 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.937534 -0.0561857 -0.0206715 0.0509115 0.928048 -0.200673 0.0314986 0.199261 0.91214 Offset = [2.90243, -3.45224, 30.9454] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.939223 -0.0695123 -0.0469228 0.114742 0.927727 -0.180151 0.041014 0.190403 0.912421 Offset = [3.36362, -2.89717, 31.4428] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 25 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.933818 -0.0666416 -0.0419474 0.124655 0.925104 -0.18078 0.0375484 0.184638 0.912372 Offset = [3.46569, -2.51521, 31.4859] Background level guess : first place: 0 (99.9727%) second place: 101 (0.0016276%) Guessed background level: 0 [AtlasCreator 18:42:38] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:42:39] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:42:39] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG33.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG33.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 337 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 227 LowHigh Thresholds: [0,84.7656,227] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x17bc340) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4078 Debug: Off Observers: none Matrix: 0.978148 -0.206773 0.0217327 0.207912 0.972789 -0.102244 1.73472e-18 0.104528 0.994522 Offset: [-1.96541, -1.98156, 25.8151] Center: [0.185029, 12.049, -0.973908] Translation: [-4.48202, -2.17137, 27.0798] Inverse: 0.978148 0.207912 1.73472e-18 -0.206773 0.972789 0.104528 0.0217327 -0.102244 0.994522 Singular: 0 Versor: [ 0.0520493, 0.0054706, 0.104385, 0.993159 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 105 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.985864 -0.163356 0.0372458 0.166536 0.979792 -0.110784 -0.0183958 0.115421 0.993146 Offset = [-2.47412, -1.46738, 25.2183] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 53 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.935985 -0.148597 0.0340407 0.151084 0.917834 -0.0887094 -0.0203323 0.0928156 0.983289 Offset = [-2.48632, -0.717675, 25.9438] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 15 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.936027 -0.159314 0.0321307 0.152625 0.912917 -0.138005 -0.0185014 0.0901214 0.974741 Offset = [-2.68341, -1.00204, 26.0565] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 19 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.930764 -0.161877 0.0322411 0.143379 0.909389 -0.143229 -0.0179428 0.102122 0.979087 Offset = [-2.61651, -0.984445, 26.0363] Background level guess : first place: 0 (99.8485%) second place: 76 (0.00217014%) Guessed background level: 0 [AtlasCreator 18:47:09] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:47:10] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:47:10] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG4.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG4.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 299 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 205 LowHigh Thresholds: [0,75.9375,205] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x1f366c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4078 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-0.158523, -6.57891, 34.4457] Center: [0.185029, 12.049, -0.973908] Translation: [-0.786188, -6.64647, 36.9721] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 27 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997665 -0.0664419 -0.0157817 0.0588413 0.953642 -0.295137 0.0346595 0.293519 0.955325 Offset = [-0.499191, -5.61023, 33.4671] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 20 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.861076 -0.0322763 -0.0643285 0.0155975 0.928408 -0.2446 0.0702612 0.242963 0.830771 Offset = [-0.77777, -5.57672, 34.5793] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 33 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.858096 -0.0329034 -0.0442433 0.0447109 0.918189 -0.284692 0.069806 0.238447 0.8202 Offset = [-0.836226, -5.66193, 34.5295] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.856859 -0.0372692 -0.0484828 0.0467061 0.92092 -0.274685 0.0820061 0.240829 0.818 Offset = [-0.877558, -5.40885, 34.5558] Background level guess : first place: 0 (99.959%) second place: 76 (0.00139509%) Guessed background level: 0 [AtlasCreator 18:51:18] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:51:18] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:51:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG5.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG5.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 332 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 223 LowHigh Thresholds: [0,82.5,223] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x19906c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4081 Debug: Off Observers: none Matrix: 0.994522 -0.102244 0.0217327 0.104528 0.972789 -0.206773 1.73472e-18 0.207912 0.978148 Offset: [2.93766, -2.37639, 21.811] Center: [0.185029, 12.049, -0.973908] Translation: [1.68355, -2.48354, 24.3374] Inverse: 0.994522 0.104528 1.73472e-18 -0.102244 0.972789 0.207912 0.0217327 -0.206773 0.978148 Singular: 0 Versor: [ 0.104385, 0.0054706, 0.0520493, 0.993159 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 50 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.997755 -0.0624664 -0.0241634 0.0508572 0.941355 -0.333562 0.0435828 0.331584 0.942418 Offset = [2.56395, -2.45486, 18.9325] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.946897 -0.0600945 -0.0254498 0.0519398 0.873272 -0.247824 0.0395133 0.245974 0.873076 Offset = [2.63542, -0.471098, 21.1749] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 21 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.946512 -0.061926 -0.0201771 0.0706673 0.864312 -0.270176 0.0471311 0.234525 0.867094 Offset = [2.31943, -0.224107, 21.6189] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 38 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.946706 -0.0576993 -0.0196353 0.0673276 0.881558 -0.271058 0.0464177 0.235684 0.871361 Offset = [2.51925, -0.401039, 21.3415] Background level guess : first place: 0 (99.998%) second place: 84 (0.00031002%) Guessed background level: 0 [AtlasCreator 18:55:39] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 18:55:40] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 18:55:40] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG6.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG6.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 286 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 209 LowHigh Thresholds: [0,77.25,209] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x21046c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4090 Debug: Off Observers: none Matrix: 0.994522 -0.103956 -0.0109262 0.104528 0.989074 0.103956 -8.67362e-19 -0.104528 0.994522 Offset: [-0.0145208, 0.245765, 18.7999] Center: [0.185029, 12.049, -0.973908] Translation: [-1.25745, 0.0322131, 17.5458] Inverse: 0.994522 0.104528 -8.67362e-19 -0.103956 0.989074 -0.104528 -0.0109262 0.103956 0.994522 Singular: 0 Versor: [ -0.0522642, -0.00273905, 0.0522642, 0.997261 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 54 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.995825 -0.0863713 -0.0295499 0.0891804 0.989601 0.112859 0.0194949 -0.115023 0.993172 Offset = [-0.228634, 0.323185, 18.0327] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 60 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.874044 -0.0558701 -0.0328786 0.0593901 0.917451 0.11819 0.0259864 -0.119894 0.925278 Offset = [-0.713905, 1.3212, 19.5946] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 30 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.872887 -0.0672908 -0.0198647 0.0635216 0.92116 0.112511 0.0208119 -0.117336 0.924635 Offset = [-0.492616, 1.23214, 19.4902] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.875993 -0.0726914 -0.026417 0.073804 0.922738 0.114962 0.0226516 -0.115176 0.93263 Offset = [-0.400572, 1.32793, 19.1557] Background level guess : first place: 0 (99.9101%) second place: 51 (0.00201513%) Guessed background level: 0 [AtlasCreator 19:00:18] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 19:00:18] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 19:00:18] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG7.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG7.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 285 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 210 LowHigh Thresholds: [0,77.5625,210] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xc3d6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4084 Debug: Off Observers: none Matrix: 0.99863 -0.0511923 0.0108813 0.052336 0.976807 -0.207627 -8.67362e-19 0.207912 0.978148 Offset: [-1.17253, -4.06194, 33.0757] Center: [0.185029, 12.049, -0.973908] Translation: [-1.8002, -4.1295, 35.6021] Inverse: 0.99863 0.052336 -8.67362e-19 -0.0511923 0.976807 0.207912 0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, 0.00273624, 0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 66 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.995813 -0.0737828 -0.0539684 0.0610304 0.976137 -0.208404 0.0680572 0.204238 0.976553 Offset = [-0.610302, -3.62145, 32.5239] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.924154 -0.0644924 -0.0679259 0.0468641 0.899628 -0.234913 0.0810985 0.230697 0.895712 Offset = [-1.06503, -3.36047, 33.2035] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 13 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.926924 -0.0680376 -0.0703669 0.0576415 0.9013 -0.247558 0.0889254 0.222074 0.885329 Offset = [-1.10678, -3.27386, 33.3755] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.916533 -0.0665226 -0.0735654 0.0556143 0.901719 -0.249427 0.084557 0.223965 0.898979 Offset = [-1.03645, -3.33874, 33.5555] Guessed background level: 0 [AtlasCreator 19:04:36] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 19:04:37] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 19:04:37] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG8.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG8.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 288 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 193 LowHigh Thresholds: [0,71.3672,193] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0xefd6c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4081 Debug: Off Observers: none Matrix: 0.99863 0.0511923 -0.0108813 -0.052336 0.976807 -0.207627 8.67362e-19 0.207912 0.978148 Offset: [-1.60661, -4.931, 27.2064] Center: [0.185029, 12.049, -0.973908] Translation: [-0.979451, -5.01793, 29.7328] Inverse: 0.99863 -0.052336 8.67362e-19 0.0511923 0.976807 0.207912 -0.0108813 -0.207627 0.978148 Singular: 0 Versor: [ 0.104493, -0.00273624, -0.0260335, 0.994181 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 34 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.998009 0.0380989 -0.0502714 -0.0472792 0.979391 -0.196361 0.0417542 0.198347 0.979242 Offset = [-1.37226, -4.81528, 27.2504] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 31 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.885384 0.0273727 -0.0492867 -0.0350493 0.903464 -0.162336 0.0441586 0.163805 0.880434 Offset = [-1.44187, -3.62067, 28.0328] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 36 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.879411 0.0292716 -0.0587643 9.91978e-05 0.896235 -0.194717 0.0508364 0.154248 0.864203 Offset = [-1.56495, -3.44092, 28.738] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 14 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.877427 0.035271 -0.0499996 0.00991871 0.894766 -0.203302 0.0498215 0.165727 0.871143 Offset = [-1.5977, -3.29404, 28.6163] Guessed background level: 0 [AtlasCreator 19:08:50] DEBUG: Guessing background value: 0.0 Background level guess : first place: 0 (99.7032%) second place: 148 (0.00596788%) Guessed background level: 0 [AtlasCreator 19:08:51] DEBUG: Guessing background value for template: 0.0 [AtlasCreator 19:08:51] DEBUG: Register command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSFit --fixedVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --movingVolume /projects/na-mic/haehn/DATASETS/Study/originals/caseG9.nrrd --outputTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/LSGNnJAtlasCreator/caseG9.nrrd --maxBSplineDisplacement 10.0 --outputVolumePixelType short --interpolationMode Linear --initializeTransformMode useCenterOfHeadAlign --useRigid --useScaleVersor3D --useScaleSkewVersor3D --useAffine --debugNumberOfThreads -1 --backgroundFillValue 0.0 --numberOfSamples 100000 --numberOfIterations 1500 --translationScale 1000.0 --reproportionScale 1.0 --skewScale 1.0 --splineGridSize 28,20,24 --fixedVolumeTimeIndex 0 --movingVolumeTimeIndex 0 --medianFilterSize 0,0,0 --numberOfHistogramBins 50 --numberOfMatchPoints 10 --useCachingOfBSplineWeightsMode ON --useExplicitPDFDerivativesMode AUTO --relaxationFactor 0.5 --failureExitCode -1 --debugLevel 0 --costFunctionConvergenceFactor 1e+9 --projectedGradientTolerance 1e-5 Original Fixed image origin[-120, 93, 120, 0] TranformTypes: Rigid(1 of 4). TranformTypes: ScaleVersor3D(2 of 4). TranformTypes: ScaleSkewVersor3D(3 of 4). TranformTypes: Affine(4 of 4). Initializing transform with useCenterOfHeadAlign ListSample TotalFrequency is 8126464 305 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 198 LowHigh Thresholds: [0,70.8906,198] maxSIDirection = 120 Computing Sampled Distance Computations ListSample TotalFrequency is 8126464 271 ValidHistogramsEntries, 8126464 TotalFrequency 0.001 ---> 0 0.999 ---> 176 LowHigh Thresholds: [0,63.2109,176] maxSIDirection = 120 Computing Sampled Distance Computations Initializing transform with useCenterOfHeadAlign to VersorRigid3DTransform (0x22b86c0) RTTI typeinfo: itk::VersorRigid3DTransform Reference Count: 2 Modified Time: 4054 Debug: Off Observers: none Matrix: 0.99863 -0.052336 7.26307e-19 0.052336 0.99863 -1.38588e-17 0 1.38778e-17 1 Offset: [-2.24373, -5.0741, 30.4672] Center: [0.185029, 12.049, -0.973908] Translation: [-2.87458, -5.08092, 30.4672] Inverse: 0.99863 0.052336 0 -0.052336 0.99863 1.38778e-17 7.26307e-19 -1.38588e-17 1 Singular: 0 Versor: [ 6.93652e-18, 1.81639e-19, 0.0261769, 0.999657 ] =============================================== =============================== Starting Transform Estimations for Rigid(1 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.VersorRigid3DTransformOptimizer: Step too small after 57 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.994108 -0.0516132 -0.0953212 0.0522068 0.998629 0.00374168 0.0949975 -0.00869605 0.99544 Offset = [-2.10129, -6.29547, 29.5766] =============================== Starting Transform Estimations for ScaleVersor3D(2 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 28 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.918372 -0.0345725 -0.0973315 0.0347999 0.881856 0.000639456 0.0972504 -0.00402316 0.915749 Offset = [-2.31999, -2.79252, 30.5758] =============================== Starting Transform Estimations for ScaleSkewVersor3D(3 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 0.001, 0.001, 0.001, 1, 1, 1, 1, 1, 1, 1, 1, 1]. Stop condition from optimizer.VersorTransformOptimizer: Step too small after 32 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.922354 -0.0355643 -0.0951005 0.0788009 0.878613 -0.0219788 0.0816117 -0.0256793 0.91202 Offset = [-2.36604, -2.91199, 30.6995] =============================== Starting Transform Estimations for Affine(4 of 4).=============================== Initializer, optimizerScales: [1, 1, 1, 1, 1, 1, 1, 1, 1, 0.001, 0.001, 0.001]. Stop condition from optimizer.RegularStepGradientDescentOptimizer: Step too small after 22 iterations. Current step (0.003125) is less than minimum step (0.005). Matrix = 0.924259 -0.0304105 -0.0961932 0.0809699 0.881517 -0.0335271 0.0766294 -0.00457641 0.915966 Offset = [-2.45924, -2.79896, 30.537] [AtlasCreator 19:13:11] Waiting for Registration to complete.. [AtlasCreator 19:13:16] DEBUG: All outputs exist! [AtlasCreator 19:13:16] Saving template to /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/template.nrrd [AtlasCreator 19:13:17] Entering Resampling Stage.. [AtlasCreator 19:13:17] Found 3D Slicer launcher at /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 [AtlasCreator 19:13:17] DEBUG: The launchCommandPrefix is /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/ Guessed background level: 0 [AtlasCreator 19:13:18] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:18] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case10.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case10.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case10.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case10.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case10.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case10.mat Guessed background level: 0 [AtlasCreator 19:13:21] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:21] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case12.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case12.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case12.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case12.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case12.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case12.mat Guessed background level: 0 [AtlasCreator 19:13:24] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:24] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case14.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case14.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case14.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case14.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case14.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case14.mat Guessed background level: 0 [AtlasCreator 19:13:27] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:27] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case15.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case15.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case15.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case15.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case15.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case15.mat Guessed background level: 0 [AtlasCreator 19:13:30] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:30] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case19.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case19.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case19.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case19.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case19.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case19.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case19.mat Guessed background level: 0 [AtlasCreator 19:13:34] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:34] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case2.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case2.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case2.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case2.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case2.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case2.mat Guessed background level: 0 [AtlasCreator 19:13:37] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:37] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case20.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case20.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case20.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case20.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case20.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case20.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case20.mat Guessed background level: 0 [AtlasCreator 19:13:39] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:39] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case23.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case23.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case23.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case23.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case23.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case23.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case23.mat Guessed background level: 0 [AtlasCreator 19:13:42] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:42] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case26.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case26.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case26.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case26.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case26.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case26.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case26.mat Guessed background level: 0 [AtlasCreator 19:13:45] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:45] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case27.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case27.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case27.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case27.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case27.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case27.mat Guessed background level: 0 [AtlasCreator 19:13:49] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:49] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case29.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case29.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case29.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case29.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case29.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case29.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case29.mat Guessed background level: 0 [AtlasCreator 19:13:52] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:52] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case3.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case3.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case3.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case3.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case3.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case3.mat Guessed background level: 0 [AtlasCreator 19:13:56] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:56] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case32.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case32.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case32.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case32.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case32.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case32.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case32.mat Guessed background level: 0 [AtlasCreator 19:13:59] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:13:59] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case33.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case33.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case33.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case33.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case33.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case33.mat Guessed background level: 0 [AtlasCreator 19:14:02] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:02] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case36.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case36.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case36.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case36.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case36.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case36.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case36.mat Guessed background level: 0 [AtlasCreator 19:14:06] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:06] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case40.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case40.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case40.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case40.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case40.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case40.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case40.mat Guessed background level: 0 [AtlasCreator 19:14:09] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:09] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case41.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case41.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case41.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case41.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case41.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case41.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case41.mat Guessed background level: 0 [AtlasCreator 19:14:13] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:13] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case42.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case42.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case42.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case42.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case42.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case42.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case42.mat Guessed background level: 0 [AtlasCreator 19:14:17] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:17] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case46.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case46.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case46.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case46.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case46.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case46.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case46.mat Guessed background level: 0 [AtlasCreator 19:14:20] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:20] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case47.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case47.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case47.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case47.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case47.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case47.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case47.mat Guessed background level: 0 [AtlasCreator 19:14:24] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:24] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case48.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case48.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case48.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case48.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case48.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case48.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case48.mat Guessed background level: 0 [AtlasCreator 19:14:28] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:28] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case51.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case51.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case51.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case51.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case51.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case51.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case51.mat Guessed background level: 0 [AtlasCreator 19:14:32] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:32] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case53.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case53.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case53.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case53.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case53.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case53.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case53.mat Guessed background level: 0 [AtlasCreator 19:14:35] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:35] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case54.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case54.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case54.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case54.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case54.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case54.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case54.mat Guessed background level: 0 [AtlasCreator 19:14:39] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:39] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case57.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case57.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case57.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case57.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case57.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case57.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case57.mat Guessed background level: 0 [AtlasCreator 19:14:42] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:42] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case59.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case59.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case59.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case59.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case59.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case59.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case59.mat Guessed background level: 0 [AtlasCreator 19:14:45] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:45] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case60.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case60.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case60.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case60.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case60.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case60.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case60.mat Guessed background level: 0 [AtlasCreator 19:14:48] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:48] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case61.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case61.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case61.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case61.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case61.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case61.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case61.mat Guessed background level: 0 [AtlasCreator 19:14:51] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:51] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case62.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case62.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case62.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case62.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case62.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case62.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case62.mat Guessed background level: 0 [AtlasCreator 19:14:54] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:54] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/case8.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case8.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/case8.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/case8.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case8.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/case8.mat Guessed background level: 0 [AtlasCreator 19:14:58] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:14:58] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG1.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG1.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG1.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG1.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG1.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG1.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG1.mat Guessed background level: 0 [AtlasCreator 19:15:01] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:01] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG10.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG10.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG10.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG10.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG10.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG10.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG10.mat Guessed background level: 0 [AtlasCreator 19:15:04] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:04] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG11.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG11.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG11.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG11.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG11.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG11.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG11.mat Guessed background level: 0 [AtlasCreator 19:15:07] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:07] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG12.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG12.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG12.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG12.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG12.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG12.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG12.mat Guessed background level: 0 [AtlasCreator 19:15:10] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:10] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG13.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG13.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG13.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG13.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG13.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG13.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG13.mat Guessed background level: 0 [AtlasCreator 19:15:14] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:14] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG14.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG14.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG14.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG14.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG14.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG14.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG14.mat Guessed background level: 0 [AtlasCreator 19:15:17] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:17] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG15.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG15.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG15.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG15.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG15.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG15.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG15.mat Guessed background level: 0 [AtlasCreator 19:15:20] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:20] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG16.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG16.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG16.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG16.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG16.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG16.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG16.mat Guessed background level: 0 [AtlasCreator 19:15:23] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:23] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG17.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG17.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG17.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG17.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG17.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG17.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG17.mat Guessed background level: 0 [AtlasCreator 19:15:27] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:27] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG2.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG2.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG2.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG2.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG2.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG2.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG2.mat Guessed background level: 0 [AtlasCreator 19:15:30] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:30] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG27.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG27.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG27.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG27.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG27.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG27.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG27.mat Guessed background level: 0 [AtlasCreator 19:15:33] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:33] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG3.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG3.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG3.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG3.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG3.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG3.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG3.mat Guessed background level: 0 [AtlasCreator 19:15:36] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:36] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG33.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG33.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG33.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG33.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG33.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG33.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG33.mat Guessed background level: 0 [AtlasCreator 19:15:40] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:40] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG4.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG4.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG4.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG4.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG4.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG4.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG4.mat Guessed background level: 0 [AtlasCreator 19:15:43] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:43] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG5.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG5.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG5.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG5.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG5.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG5.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG5.mat Guessed background level: 0 [AtlasCreator 19:15:46] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:46] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG6.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG6.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG6.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG6.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG6.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG6.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG6.mat Guessed background level: 0 [AtlasCreator 19:15:49] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:49] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG7.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG7.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG7.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG7.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG7.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG7.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG7.mat Guessed background level: 0 [AtlasCreator 19:15:52] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:52] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG8.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG8.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG8.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG8.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG8.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG8.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG8.mat Guessed background level: 0 [AtlasCreator 19:15:55] DEBUG: Guessing background value: 0.0 [AtlasCreator 19:15:55] DEBUG: Resample command: /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/Slicer3 --launch /var/tmp/haehn/SLICER/TRUNK/Slicer3-build/lib/Slicer3/Plugins/BRAINSResample --inputVolume /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG9.nrrd --referenceVolume /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd --warpTransform /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG9.mat --outputVolume /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG9.nrrd --defaultValue 0.0 --pixelType short --interpolationMode NearestNeighbor ===================================================== Input Volume: /projects/na-mic/haehn/DATASETS/Study/segmentations/caseG9.nrrd Reference Volume: /projects/na-mic/haehn/DATASETS/Study/originals/case5.nrrd Output Volume: /var/tmp/haehn/Slicer3haehn/b3jzN9AtlasCreatorResampled/caseG9.nrrd Pixel Type: short Interpolation: NearestNeighbor Background Value: 0 Warp By Transform: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG9.mat ===================================================== Read ITK transform from text file: /projects/na-mic/haehn/DATASETS/Study/brainsfitFixed/caseG9.mat [AtlasCreator 19:15:58] Entering Combine-To-Atlas Stage.. [AtlasCreator 19:16:25] Re-Casting atlas for label 32 to Short [AtlasCreator 19:17:01] Re-Casting atlas for label 3 to Short [AtlasCreator 19:17:44] Re-Casting atlas for label 4 to Short [AtlasCreator 19:18:41] Re-Casting atlas for label 5 to Short [AtlasCreator 19:19:51] Re-Casting atlas for label 6 to Short [AtlasCreator 19:21:22] Re-Casting atlas for label 7 to Short [AtlasCreator 19:23:23] Re-Casting atlas for label 8 to Short [AtlasCreator 19:25:57] Re-Casting atlas for label 9 to Short [AtlasCreator 19:29:14] Re-Casting atlas for label 10 to Short [AtlasCreator 19:33:19] Re-Casting atlas for label 31 to Short [AtlasCreator 19:33:19] Re-Casting atlas to Short [AtlasCreator 19:33:20] -------------------------------------------------------------------------------- [AtlasCreator 19:33:20] All Done, folks! [AtlasCreator 19:33:20] -------------------------------------------------------------------------------- Generic Warning: In /var/tmp/haehn/SLICER/TRUNK/Slicer3-lib/VTK/Common/vtkDebugLeaks.cxx, line 296 Deleting unknown object: vtkSlicerApplication